ORIGINAL: Rainer
Cargo is civilian, Transport under military control.
Thus transports have a better chance to press on in case of enemy threat, while cargo will - or at least should - withdraw or abort mission.
Note: this is based on original WitP, but I suspect that has not changed.
Interesting take. I did not know this.
I've been playing under the impression that Cargo was really there for resources and oil hauling, just to administratively allow the player to see each kind of role for moving TFs, and since the Allies don't need to haul either, I never use Cargo for anything. All Transport for supplies and air groups. Either Tanker or Transport for fuel.
Without divulging code or algorithms, if a dev could confirm the above quote I think a lot of Allied players would change their TF formation habits.
Page 77 of the PDF manuals says only: "Cargo. These TFs are meant to carry supplies and resources. Maximum of 100 ships per TF." Nothing about TF behavior under threat. Doing a find search also shows the manual making a distinction between capital-C Cargo and small-c cargo, with the latter being interchangable with supplies, LCU devices, and sometimes liquid cargo.
Any dev clarification welcome.